1
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Mehrdad SA, Cucchiarini A, Mergny JL, Noureini SK. Heavy metal ions interactions with G-quadruplex-prone DNA sequences. Biochimie 2024:S0300-9084(24)00123-8. [PMID: 38821199 DOI: 10.1016/j.biochi.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
The industrial world exposes living organisms to a variety of metal pollutants. Here we investigated whether such elements affect G-rich sequences susceptible to fold into G-quadruplex (GQ) structures. Thermal stability and conformation of these oligoncleotides was studied at various molar ratios of a variety of heavy metal salts using thermal FRET, transition-FRET (t-FRET) and circular dichroism. Metal ions affected the thermal stability of the GQs to different extents; some metals had no effect on Tm while other metals caused small to moderate changes in Tm at 1:1 or 1:10 molar ratio. While most of the metals had no major effect, Al3+, Cd2+, Pb2+, Hg2+ and Zn2+ altered the thermal stability and structural features of the GQs. Some metals such as Pb2+ and Hg2+ exhibit differential interactions with telomere, c-myc and c-kit GQs. Overall, toxic heavy metals affect G-quadruplex stability in a sequence and topology dependent manner. This study provides new insight into how heavy metal exposure may affect gene expression and cellular responses.
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Affiliation(s)
- Seyyed-Ali Mehrdad
- Department of Biology, Faculty of Basic Science, Hakim Sabzevari University, Sabzevar, Iran
| | - Anne Cucchiarini
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Sakineh Kazemi Noureini
- Department of Biology, Faculty of Basic Science, Hakim Sabzevari University, Sabzevar, Iran.
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2
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Vogelauer M, Cheng C, Karimian A, Iranpour HG, Kurdistani SK. Zinc is Essential for the Copper Reductase Activity of Yeast Nucleosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557765. [PMID: 37745536 PMCID: PMC10515886 DOI: 10.1101/2023.09.14.557765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The histone H3-H4 tetramer is a copper reductase enzyme, facilitating the production of cuprous (Cu1+) ions for distribution to copper-dependent enzymes. It was, however, unknown if this enzymatic activity occurred within nucleosomes. To investigate this, we obtained native nucleosomes from Saccharomyces cerevisiae using micrococcal nuclease digestion of chromatin in isolated nuclei and ion-exchange chromatographic purification. The purified nucleosomal fragments robustly reduced Cu2+ to Cu1+ ions, with the optimal activity dependent on the presence of zinc ions. Mutation of the histone H3 histidine 113 (H3H113) residue at the active site substantially reduced the enzymatic activity of nucleosomes, underscoring the catalytic role of histone H3. Consistently, limiting zinc ions reduced intracellular Cu1+ levels and compromised growth, phenotypes that were mitigated by genetically enhancing the copper reductase activity of histone H3. These results indicate that yeast nucleosomes possess copper reductase activity, suggesting that the fundamental unit of eukaryotic chromatin is an enzyme complex.
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Affiliation(s)
- Maria Vogelauer
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Chen Cheng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ansar Karimian
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Hooman Golshan Iranpour
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Siavash K. Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
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3
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Swaminathan S, Karvembu R. Dichloro Ru(II)- p-cymene-1,3,5-triaza-7-phosphaadamantane (RAPTA-C): A Case Study. ACS Pharmacol Transl Sci 2023; 6:982-996. [PMID: 37470017 PMCID: PMC10353064 DOI: 10.1021/acsptsci.3c00085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Indexed: 07/21/2023]
Abstract
The use of organometallic compounds to treat various phenotypes of cancer has attracted increased interest in recent decades. Organometallic compounds, which are transitional between conventional inorganic and organic materials, have outstanding and one-of-a-kind features that offer fresh insight into the development of inorganic medicinal chemistry. The therapeutic potential of ruthenium(II)-arene RAPTA-type compounds is being thoroughly investigated, specifically owing to the excellent antimetastatic property of the initial candidate RAPTA-C. This review gives a thorough analysis of this complex and its evolution as a potential anticancer drug candidate. The numerous mechanistic investigations of RAPTA-C are discussed, and they are connected to the macroscopic biological characteristics that have been found. The "multitargeted" complex described here target enzymes, peptides, and intracellular proteins in addition to DNA that allow it to specifically target cancer cells. Understanding these may allow researchers to find specific targets and tune a new-generation organometallic complex accordingly.
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Affiliation(s)
- Srividya Swaminathan
- Department
of Chemistry, National Institute of Technology, Tiruchirappalli 620015, Tamil Nadu, India
- Center
for Computational Modeling, Chennai Institute
of Technology (CIT), Chennai 600069, India
| | - Ramasamy Karvembu
- Department
of Chemistry, National Institute of Technology, Tiruchirappalli 620015, Tamil Nadu, India
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4
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Mansouri F, Ortiz D, Dyson PJ. Competitive binding studies of the nucleosomal histone targeting drug, [Ru(η 6-p-cymene)Cl 2(pta)] (RAPTA-C), with oligonucleotide-peptide mixtures. J Inorg Biochem 2023; 238:112043. [PMID: 36370502 DOI: 10.1016/j.jinorgbio.2022.112043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 11/07/2022]
Abstract
Protein crystallography and biochemical assays reveal that the organometallic drug, [Ru(η6-p-cymene)Cl2(pta)] (RAPTA-C), preferentially binds to nucleosomal histone proteins in chromatin. To better understand the binding mechanism we report here a mass spectrometric-based competitive binding study between a model peptide from the acidic patch region of the H2A histone protein (the region where RAPTA-C is known to bind) and an oligonucleotide. In contrast to the protein crystallography and biochemical assays, RAPTA-C preferentially binds to the oligonucleotide, confirming that steric factors, rather than electronic effects, primarily dictate binding of RAPTA-C to histone proteins within the nucleosome.
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Affiliation(s)
- Farangis Mansouri
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne CH-1015, Switzerland; Department of Chemistry Institute for Advanced Studies in Basic Sciences (IASBS), 444 Prof. Sobouti Blvd., Gava Zang, Zanjan 45137-66731, Iran
| | - Daniel Ortiz
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Paul J Dyson
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne CH-1015, Switzerland.
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5
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Stone S, Ray D, Andricioaei I. Force-Field-Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA. J Chem Inf Model 2022; 62:6749-6761. [PMID: 36049242 PMCID: PMC9795553 DOI: 10.1021/acs.jcim.2c00519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Hoogsteen (HG) base pairing conformation, commonly observed in damaged and mutated DNA helices, facilitates DNA repair and DNA recognition. The free energy difference between HG and Watson-Crick (WC) base pairs has been computed in previous studies. However, the mechanism of the conformational transition is not well understood. A detailed understanding of the process of WC to HG base pair transition can provide a deeper understanding of DNA repair and recognition. In an earlier study, we explored the free energy landscape for this process using extensive computer simulation with the CHARMM36 force field. In this work, we study the impact of force field models in describing the WC to HG base pairing transition using meta-eABF enhanced sampling, quasi-harmonic entropy calculation, and nonbonded energy analysis. The secondary structures of both base pairing forms and the topology of the free energy landscapes were consistent over different force field models, although the relative free energy, entropy, and the interaction energies tend to vary. The relative stability of the WC and HG conformations is dictated by a delicate balance between the enthalpic stabilization and the reduced entropy of the structurally rigid HG structure. These findings highlight the impact that subtleties in force field models can have on accurately modeling DNA base pair dynamics and should stimulate further computational investigations into other dynamically important motions in DNA.
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Affiliation(s)
- Sharon
Emily Stone
- Department
of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Dhiman Ray
- Department
of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Ioan Andricioaei
- Department
of Chemistry, University of California Irvine, Irvine, California 92697, United States,Department
of Physics and Astronomy, University of
California Irvine, Irvine, California 92697, United States,
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6
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Simultaneous mass spectrometry analysis of cisplatin with oligonucleotide-peptide mixtures: implications for the mechanism of action. J Biol Inorg Chem 2022; 27:239-248. [PMID: 35064831 PMCID: PMC8907109 DOI: 10.1007/s00775-022-01924-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/30/2021] [Indexed: 11/03/2022]
Abstract
AbstractAlthough genomic DNA is the primary target of anticancer platinum-based drugs, interactions with proteins also play a significant role in their overall activity. In this study, competitive binding of cisplatin with an oligonucleotide and two peptides corresponding to segments of H2A and H2B histone proteins was investigated by mass spectrometry. Following the determination of the cisplatin binding sites on the oligonucleotide and peptides by tandem mass spectrometry, competitive binding was studied and transfer of platinum fragments from the platinated peptides to the oligonucleotide explored. In conjunction with previous studies on the nucleosome, the results suggest that all four of the abundant histone proteins serve as a platinum drug reservoir in the cell nucleus, providing an adduct pool that can be ultimately transferred to the DNA.
Graphical abstract
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7
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Lin Z, Zheng Y, Deng F, Luo X, Zou J, Shao P, Zhang S, Tang H. Target-directed design of dual-functional Z-scheme AgIn5S8/SnS2 heterojunction for Pb(II) capture and photocatalytic reduction of Cr(VI): Performance and mechanism insight. Sep Purif Technol 2021. [DOI: 10.1016/j.seppur.2021.119430] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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8
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Vaiserman A, Lushchak O. DNA methylation changes induced by prenatal toxic metal exposure: An overview of epidemiological evidence. ENVIRONMENTAL EPIGENETICS 2021; 7:dvab007. [PMID: 34631153 PMCID: PMC8493661 DOI: 10.1093/eep/dvab007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/06/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
Accumulating evidence suggests that exposure to unfavorable conditions early in life can substantially contribute to the risk of chronic disorders later in life ('developmental programming' phenomenon). The mechanistic basis for this phenomenon remains poorly understood so far, although epigenetic mechanisms such as DNA methylation, histone modifications and microRNA-mediated gene regulation apparently play a crucial role. The key role of epigenetic modifications triggered by unfavorable environmental cues during sensitive developmental periods in linking adverse early-life events to later-life health outcomes is evident from a large body of studies, including methylome-wide association studies and research of candidate genes. Toxic metals (TMs), such as heavy metals, including lead, chromium, cadmium, arsenic, mercury, etc., are among environmental contaminants currently most significantly impacting human health status. Since TMs can cross the placental barrier and accumulate in fetal tissues, exposure to high doses of these xenobiotics early in development is considered to be among important factors contributing to the developmental programming of adult-life diseases in modern societies. In this mini-review, we summarize epidemiological findings indicating that prenatal TM exposure can induce epigenetic dysregulation, thereby potentially affecting adult health outcomes.
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Affiliation(s)
- Alexander Vaiserman
- Laboratory of Epigenetics, D.F. Chebotarev Institute of Gerontology, NAMS, 67 Vyshgorodska str., Kyiv 04114, Ukraine
| | - Oleh Lushchak
- *Correspondence address. Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenka str., Ivano-Frankivsk 76018, Ukraine. Tel/Fax: +38 0342 71 46 83; E-mail:
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9
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Montano L, Donato F, Bianco PM, Lettieri G, Guglielmino A, Motta O, Bonapace IM, Piscopo M. Semen quality as a potential susceptibility indicator to SARS-CoV-2 insults in polluted areas. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:37031-37040. [PMID: 34053043 PMCID: PMC8164491 DOI: 10.1007/s11356-021-14579-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/21/2021] [Indexed: 05/11/2023]
Abstract
The epidemic of the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has impacted worldwide with its infectious spread and mortality rate. Thousands of articles have been published to tackle this crisis and many of these have indicated that high air pollution levels may be a contributing factor to high outbreak rates of COVID-19. Atmospheric pollutants, indeed, producing oxidative stress, inflammation, immuno-unbalance, and systemic coagulation, may be a possible significant co-factor of further damage, rendering the body prone to infections by a variety of pathogens, including viruses. Spermatozoa are extremely responsive to prooxidative effects produced by environmental pollutants and may serve as a powerful alert that signals the extent that environmental pressure, in a specific area, is doing damage to humans. In order to improve our current knowledge on this topic, this review article summarizes the relevant current observations emphasizing the weight that environmental pollution has on the sensitivity of a given population to several diseases and how semen quality, may be a potential indicator of sensitivity for virus insults (including SARS-CoV-2) in high polluted areas, and help to predict the risk for harmful effects of the SARS-CoV-2 epidemic. In addition, this review focused on the potential routes of virus transmission that may represent a population health risk and also identified the areas of critical importance that require urgent research to assess and manage the COVID-19 outbreak.
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Affiliation(s)
- Luigi Montano
- Andrology Unit, EcoFoodFertility Project, Coordination Unit, Local Health Authority (ASL) Salerno, Oliveto Citra, Via M. Clemente, 84020 Oliveto Citra, SA Italy
| | - Francesco Donato
- Department of Medical and Surgical Specialties Radiological Sciences and Public Health, Unit of Hygiene, Epidemiology, and Public Health, University of Brescia, Brescia, Italy
| | - Pietro Massimiliano Bianco
- ISPRA, Italian Institute for Environmental Protection and Research, Via Vitaliano Brancati 60, 00144 Rome, Italy
| | - Gennaro Lettieri
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy
| | | | - Oriana Motta
- Department of Medicine, Surgery and Dentistry, University of Salerno, Fisciano, Italy
| | - Ian Marc Bonapace
- Department of Biotechnology and Life Sciences, University of Insubria (VA), Varese, Italy
| | - Marina Piscopo
- Department of Biology, University of Naples Federico II, Via Cinthia 21, 80126 Napoli, Italy
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10
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Ray D, Andricioaei I. Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA. Biophys J 2020; 119:1568-1579. [PMID: 32946766 DOI: 10.1016/j.bpj.2020.08.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 05/10/2020] [Accepted: 08/25/2020] [Indexed: 10/23/2022] Open
Abstract
Genetic information is encoded in the DNA double helix, which, in its physiological milieu, is characterized by the iconical Watson-Crick nucleo-base pairing. Recent NMR relaxation experiments revealed the transient presence of an alternative, Hoogsteen (HG) base pairing pattern in naked DNA duplexes, and estimated its relative stability and lifetime. In contrast with DNA, such structures were not observed in RNA duplexes. Understanding HG base pairing is important because the underlying "breathing" motion between the two conformations can significantly modulate protein binding. However, a detailed mechanistic insight into the transition pathways and kinetics is still missing. We performed enhanced sampling simulation (with combined metadynamics and adaptive force-bias method) and Markov state modeling to obtain accurate free energy, kinetics, and the intermediates in the transition pathway between Watson-Crick and HG base pairs for both naked B-DNA and A-RNA duplexes. The Markov state model constructed from our unbiased MD simulation data revealed previously unknown complex extrahelical intermediates in the seemingly simple process of base flipping in B-DNA. Extending our calculation to A-RNA, for which HG base pairing is not observed experimentally, resulted in relatively unstable, single-hydrogen-bonded, distorted Hoogsteen-like bases. Unlike B-DNA, the transition pathway primarily involved base paired and intrahelical intermediates with transition timescales much longer than that of B-DNA. The seemingly obvious flip-over reaction coordinate (i.e., the glycosidic torsion angle) is unable to resolve the intermediates. Instead, a multidimensional picture involving backbone dihedral angles and distance between hydrogen bond donor and acceptor atoms is required to gain insight into the molecular mechanism.
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Affiliation(s)
| | - Ioan Andricioaei
- Department of Chemistry; Department of Physics and Astronomy, University of California Irvine, Irvine, California.
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11
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Soman A, Liew CW, Teo HL, Berezhnoy NV, Olieric V, Korolev N, Rhodes D, Nordenskiöld L. The human telomeric nucleosome displays distinct structural and dynamic properties. Nucleic Acids Res 2020; 48:5383-5396. [PMID: 32374876 PMCID: PMC7261157 DOI: 10.1093/nar/gkaa289] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/01/2020] [Accepted: 05/05/2020] [Indexed: 12/21/2022] Open
Abstract
Telomeres protect the ends of our chromosomes and are key to maintaining genomic integrity during cell division and differentiation. However, our knowledge of telomeric chromatin and nucleosome structure at the molecular level is limited. Here, we aimed to define the structure, dynamics as well as properties in solution of the human telomeric nucleosome. We first determined the 2.2 Å crystal structure of a human telomeric nucleosome core particle (NCP) containing 145 bp DNA, which revealed the same helical path for the DNA as well as symmetric stretching in both halves of the NCP as that of the 145 bp ‘601’ NCP. In solution, the telomeric nucleosome exhibited a less stable and a markedly more dynamic structure compared to NCPs containing DNA positioning sequences. These observations provide molecular insights into how telomeric DNA forms nucleosomes and chromatin and advance our understanding of the unique biological role of telomeres.
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Affiliation(s)
- Aghil Soman
- School of Biological Sciences, Nanyang Technology University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Chong Wai Liew
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Hsiang Ling Teo
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Nikolay V Berezhnoy
- School of Biological Sciences, Nanyang Technology University, 60 Nanyang Drive, Singapore 637551, Singapore.,Singapore Centre for Environmental Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Vincent Olieric
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technology University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Daniela Rhodes
- School of Biological Sciences, Nanyang Technology University, 60 Nanyang Drive, Singapore 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore.,School of Chemical and Biomolecular Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technology University, 60 Nanyang Drive, Singapore 637551, Singapore
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12
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Tan X, Ravasio A, Ong HT, Wu J, Hew CL. White spot syndrome viral protein VP9 alters the cellular higher-order chromatin structure. FASEB Bioadv 2020; 2:264-279. [PMID: 32259052 PMCID: PMC7133739 DOI: 10.1096/fba.2019-00086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 10/26/2019] [Accepted: 02/05/2020] [Indexed: 12/21/2022] Open
Abstract
Viral protein 9 (VP9) is a non-structural protein of white spot syndrome virus (WSSV) highly expressed during the early stage of infection. The crystal structure of VP9 suggests that the polymers of VP9 dimers resemble a DNA mimic, but its function remains elusive. In this study, we demonstrated that VP9 impedes histones binding to DNA via single-molecule manipulation. We established VP9 expression in HeLa cells due to the lack of a WSSV-susceptible cell line, and observed abundant VP9 in the nucleus, which mirrors its distribution in the hemocytes of WSSV-infected shrimp. VP9 expression increased the dynamics and rotational mobility of histones in stable H3-GFP HeLa cells as revealed by fluorescent recovery after photobleaching and fluorescence anisotropy imaging, which suggested a loosened compaction of chromatin structure. Successive salt fractionation showed that a prominent population of histones was solubilized in high salt concentrations, which implies alterations of bulk chromatin structure. Southern blotting identified that VP9 alters juxtacentromeric chromatin structures to be more accessible to micrococcal nuclease digestion. RNA microarray revealed that VP9 expression also leads to significant changes of cellular gene expression. Our findings provide evidence that VP9 alters the cellular higher-order chromatin structure, uncovering a potential strategy adopted by WSSV to facilitate its replication.
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Affiliation(s)
- Xi Tan
- Mechanobiology InstituteNational University of SingaporeSingaporeSingapore
- Present address:
School of Basic Medical SciencesGuizhou University of Traditional Chinese MedicineGuiyangGuizhou ProvinceChina
| | - Andrea Ravasio
- Institute for Biological and Medical EngineeringSchools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiago de ChileChile
| | - Hui T. Ong
- Mechanobiology InstituteNational University of SingaporeSingaporeSingapore
| | - Jinlu Wu
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Choy L. Hew
- Mechanobiology InstituteNational University of SingaporeSingaporeSingapore
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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13
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Manduca P, Al Baraquni N, Al Baraquni L, Abu Abadi D, Abdallah H, Hamad GA, Mosa TA, Balousha S, Miqdad H, Mohammed W, Salah M, El Shawwa R. Hospital centered surveillance of births in Gaza, Palestine, 2011-2017 and heavy metal contamination of the mothers reveals long-term impact of wars. Reprod Toxicol 2019; 86:23-32. [PMID: 30844493 DOI: 10.1016/j.reprotox.2019.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 01/29/2019] [Accepted: 02/06/2019] [Indexed: 11/26/2022]
Abstract
Prevalence of preterm, low birth weight and birth defects increased significantly since 2011 in Gaza, Palestine. No change in known co-factors of reproductive health justified this rise. Two military attacks in 2012 and 2014 introduced novel risk factors for outcomes at birth: contamination by teratogenic and carcinogenic heavy metals weapon-remnants, ongoing impoverishment, and impaired rehabilitation of waste management. It was previously shown that mothers exposed to military attacks had higher metal load than those unexposed and mother's heavy metals trans-pass placenta. We investigated association in time of heavy metal contamination and reproductive health using hospital-based surveillance (2011-2016-2017) of births, accompanied by assessment in 2016 of metal load in mother and newborn hair. Mother's housing proximal to unmanaged waste predicted preterm birth and birth defects, and these women had highest load of heavy metals. Poor diet predicted low birth weight. Circumstances prevent investigation of heavy metals molecular impact(s) during fetal development.
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Affiliation(s)
| | | | | | | | | | | | | | - Suha Balousha
- Al Shifa Hospital, Gaza, Palestine; Department of Reproductive Health, Nursing and Midwifery School, International Campus, University of Medical Science, Tehran, Iran.
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14
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Lettieri G, Mollo V, Ambrosino A, Caccavale F, Troisi J, Febbraio F, Piscopo M. Molecular effects of copper on the reproductive system of mytilus galloprovincialis. Mol Reprod Dev 2019; 86:1357-1368. [PMID: 30648312 DOI: 10.1002/mrd.23114] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/11/2019] [Indexed: 01/21/2023]
Abstract
This study aims to assess the effects induced by 24 hr exposure to a subtoxic copper concentration on the reproductive system (gonads, spermatozoa, and protamine-like [PL] proteins) of Mytilus galloprovincialis. Inductively coupled plasma-mass spectrometry indicated accumulation of this metal in gonads, spermatozoa, and PL proteins of exposed mussels. Further, real-time polymerase chain reaction analyses showed altered expression levels of mt10 and PL proteins genes in spermatozoa and gonads, respectively, of exposed mussels. Protamine-like proteins, which represent the main basic component of sperm chromatin of this organism, showed a higher DNA binding affinity and a different DNA binding mode in exposed mussels. Moreover, an increased amount of NaCl was required for the release from sperm nuclei of PL-III, the main PL protein component. Finally, PL proteins extracted from exposed mussels promoted DNA oxidative damage in the presence of H 2 O 2. These results demonstrate that the tolerable copper amount could also affect the properties of PL proteins and determine the negative effects on the reproductive system of this organism. These analyses could be useful to develop quick and efficient chromatin-based genotoxicity tests for pollution biomonitoring programs.
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Affiliation(s)
- Gennaro Lettieri
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Velia Mollo
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Alessia Ambrosino
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Filomena Caccavale
- Department of Biology, University of Naples Federico II, Naples, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Jacopo Troisi
- Theoreo srl-spin-off, Company of the University of Salerno, Salerno, Italy
| | - Ferdinando Febbraio
- Institute of Protein Biochemistry, National Research Council of Italy, Naples, Italy
| | - Marina Piscopo
- Department of Biology, University of Naples Federico II, Naples, Italy
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15
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Piscopo M, Notariale R, Rabbito D, Ausió J, Olanrewaju OS, Guerriero G. Mytilus galloprovincialis (Lamarck, 1819) spermatozoa: hsp70 expression and protamine-like protein property studies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:12957-12966. [PMID: 29478169 DOI: 10.1007/s11356-018-1570-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 02/14/2018] [Indexed: 04/16/2023]
Abstract
In this work, we describe results of the reproductive health monitoring studies in Mytilus galloprovincialis following spermatozoa hsp70 expression and protamine-like protein properties. Mussels control (ctr) were released within cages for 30 days in three different marine sites near Naples (Campania, Italy): Bagnoli south (BAs) and Bagnoli north (BAn), both close to a disposal metallurgical factory and in Capo Miseno (CM). Studies of hsp70 gene expression carried out, by RT-qPCR, in mussel spermatozoa have shown varied expression levels, particularly 5, 13, and 15-fold more than ctr in CM, BAs, and BAn, respectively, indicating highest involvement of stress proteins in spermatozoa of mussels in Bagnoli. In order to evaluate the possible risk on Mytilus galloprovincialis sustainability loss, electrophoretic analyses were performed on protamine-like proteins (PL) of collected spermatozoa. The results showed that CM PL were apparently unaltered with respect to ctr PL, while BAs and BAn PL appeared in part in the form of peptides and in part as bands with low mobility. Further, CM and BAs PL showed, by electrophoretic mobility shift assay, a decrease in DNA binding ability and a change in their DNA binding mode. The results of this investigation show the usefulness of the study of alterations of spermatozoa hsp70 expression and protamine-like protein properties for eco-toxicological evaluation using Mytilus galloprovincialis as a bioindicator.
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Affiliation(s)
- Marina Piscopo
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, 80126, Naples, Italy.
| | - Rosaria Notariale
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, 80126, Naples, Italy
| | - Dea Rabbito
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, 80126, Naples, Italy
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | | | - Giulia Guerriero
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia 4, 80126, Naples, Italy
- Interdepartmental Research Center for Environment (I.R.C.Env.), Università degli Studi di Napoli, Federico II, Naples, Italy
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16
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Ferrante M, Signorelli SS, Ferlito SL, Grasso A, Dimartino A, Copat C. Groundwater-based water wells characterization from Guinea Bissau (Western Africa): A risk evaluation for the local population. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 619-620:916-926. [PMID: 29734637 DOI: 10.1016/j.scitotenv.2017.11.176] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 06/08/2023]
Abstract
The study conducted in two regions of Guinea Bissau, Oio and Cacheu, focusing on the characterization of the groundwater supplies sampled during the dry season and their associated risks for human health. Twenty samples were collected in wells located nearby pit latrines. In situ analyses were conducted with Semi-quantitative test strips for the determination of turbidity, pH, chloride, carbonate, sulfites, ammonium, nitrite and nitrate. The analysis of metals was performed by an ICP-MS Elan DRC-e and an ICP-OES Optima 8000. The Target Hazard Quotient (THQ) was applied to evaluate the risk of developing chronic systemic effects derived from exposure to metals. Values of concern of turbidity ammonium, and pH values were lower than the normal range for drinking water in most samples. From both regions, Fe and Al were occasionally found with values higher than the international thresholds fixed by the World Health Organization and by the European Commission for drinking water, while, only in one sample from Cacheu region Pb was found significantly above these limits. THQs resulted next to the level of risk (1) for the highest values found of Al, As, Fe and Mn. Of great concern is the resident risk obtained from a well water of Cacheu for the highest value of Pb (96.8μg/L), because the values of the resident risk found of 1 and 0.7 for child and adults respectively. The results obtained highlighted a close correlation between the chemistry of water and sediment and a correlation with the proximity of the water supplies with the latrines. This study evidenced the potential toxicity of the water supplies for the local populations and the risk of developing chronic systemic effects due to some physico-chemical parameters, the importance of functioning water pipeline system, the importance of maintaining adequate distance between latrines and drinking water access.
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Affiliation(s)
- Margherita Ferrante
- Department of Medical Sciences, Surgical and Advanced Technologies, "G.F. Ingrassia" - Hygiene and Public Health, Laboratory of Environmental and Food Hygiene (LIAA), University of Catania, Via S. Sofia, 87, 95123 Catania, Italy
| | - Salvatore Santo Signorelli
- Departments of Clinical and Experimental Medicine, University of Catania, Via S. Sofia, 87, 95123 Catania, Italy
| | | | - Alfina Grasso
- Department of Medical Sciences, Surgical and Advanced Technologies, "G.F. Ingrassia" - Hygiene and Public Health, Laboratory of Environmental and Food Hygiene (LIAA), University of Catania, Via S. Sofia, 87, 95123 Catania, Italy
| | - Angela Dimartino
- Department of Medical Sciences, Surgical and Advanced Technologies, "G.F. Ingrassia" - Hygiene and Public Health, Laboratory of Environmental and Food Hygiene (LIAA), University of Catania, Via S. Sofia, 87, 95123 Catania, Italy
| | - Chiara Copat
- Department of Medical Sciences, Surgical and Advanced Technologies, "G.F. Ingrassia" - Hygiene and Public Health, Laboratory of Environmental and Food Hygiene (LIAA), University of Catania, Via S. Sofia, 87, 95123 Catania, Italy.
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17
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Bao Y, Liu X, Zhang W, Cao J, Li W, Li C, Lin Z. Identification of a regulation network in response to cadmium toxicity using blood clam Tegillarca granosa as model. Sci Rep 2016; 6:35704. [PMID: 27760991 PMCID: PMC5071765 DOI: 10.1038/srep35704] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/04/2016] [Indexed: 12/19/2022] Open
Abstract
Clam, a filter-feeding lamellibranch mollusk, is capable to accumulate high levels of trace metals and has therefore become a model for investigation the mechanism of heavy metal toxification. In this study, the effects of cadmium were characterized in the gills of Tegillarca granosa during a 96-hour exposure course using integrated metabolomic and proteomic approaches. Neurotoxicity and disturbances in energy metabolism were implicated according to the metabolic responses after Cd exposure, and eventually affected the osmotic function of gill tissue. Proteomic analysis showed that oxidative stress, calcium-binding and sulfur-compound metabolism proteins were key factors responding to Cd challenge. A knowledge-based network regulation model was constructed with both metabolic and proteomic data. The model suggests that Cd stimulation mainly inhibits a core regulation network that is associated with histone function, ribosome processing and tight junctions, with the hub proteins actin, gamma 1 and Calmodulin 1. Moreover, myosin complex inhibition causes abnormal tight junctions and is linked to the irregular synthesis of amino acids. For the first time, this study provides insight into the proteomic and metabolomic changes caused by Cd in the blood clam T. granosa and suggests a potential toxicological pathway for Cd.
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Affiliation(s)
- Yongbo Bao
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, P.R. China
| | - Xiao Liu
- Department of Systems biology, GFK, Shanghai Biotech Inc., Shanghai, 201112, P.R. China
| | - Weiwei Zhang
- School of Marine Scienes, Ningbo University, Ningbo, Zhejiang, 315010, P.R. China
| | - Jianping Cao
- Ningbo Yinzhou Measurement and Test Center for Quality and Technique Supervising, Ningbo, Zhejiang, 315100, P.R. China
| | - Wei Li
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, P.R. China
| | - Chenghua Li
- School of Marine Scienes, Ningbo University, Ningbo, Zhejiang, 315010, P.R. China
| | - Zhihua Lin
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, P.R. China
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18
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Fujii Y, Wakamori M, Umehara T, Yokoyama S. Crystal structure of human nucleosome core particle containing enzymatically introduced CpG methylation. FEBS Open Bio 2016; 6:498-514. [PMID: 27419055 PMCID: PMC4865653 DOI: 10.1002/2211-5463.12064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/28/2016] [Accepted: 03/29/2016] [Indexed: 11/05/2022] Open
Abstract
Cytosine methylation, predominantly of the CpG sequence in vertebrates, is one of the major epigenetic modifications crucially involved in the control of gene expression. Due to the difficulty of reconstituting site-specifically methylated nucleosomal DNA at crystallization quality, most structural analyses of CpG methylation have been performed using chemically synthesized oligonucleotides, There has been just one recent study of nucleosome core particles (NCPs) reconstituted with nonpalindromic human satellite 2-derived DNAs. Through the preparation of a 146-bp palindromic α-satellite-based nucleosomal DNA containing four CpG dinucleotide sequences and its enzymatic methylation and restriction, we reconstituted a 'symmetric' human CpG-methylated nucleosome core particle (NCP). We solved the crystal structures of the CpG-methylated and unmodified NCPs at 2.6 and 3.0 Å resolution, respectively. We observed the electron densities of two methyl groups, among the eight 5-methylcytosines introduced in the CpG-fully methylated NCP. There were no obvious structural differences between the CpG-methylated 'symmetric NCP' and the unmodified NCP. The preparation of a crystallization-grade CpG-methylated NCP provides a platform for the analysis of CpG-methyl reader and eraser proteins.
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Affiliation(s)
- Yoshifumi Fujii
- RIKEN Systems and Structural Biology Center Tsurumi Yokohama Japan; RIKEN Structural Biology Laboratory Tsurumi Yokohama Japan
| | - Masatoshi Wakamori
- RIKEN Systems and Structural Biology Center Tsurumi Yokohama Japan; RIKEN Center for Life Science Technologies Tsurumi Yokohama Japan
| | - Takashi Umehara
- RIKEN Systems and Structural Biology CenterTsurumi Yokohama Japan; RIKEN Center for Life Science Technologies Tsurumi Yokohama Japan; PRESTO, Japan Science and Technology Agency (JST) Kawaguchi Saitama Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center Tsurumi Yokohama Japan; RIKEN Structural Biology Laboratory Tsurumi Yokohama Japan
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19
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Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S. Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation. Sci Rep 2015; 5:17204. [PMID: 26607036 PMCID: PMC4660432 DOI: 10.1038/srep17204] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/27/2015] [Indexed: 01/07/2023] Open
Abstract
Post-translational modifications (PTMs) of histones, such as lysine acetylation of the N-terminal tails, play crucial roles in controlling gene expression. Due to the difficulty in reconstituting site-specifically acetylated nucleosomes with crystallization quality, structural analyses of histone acetylation are currently performed using synthesized tail peptides. Through engineering of the genetic code, translation termination, and cell-free protein synthesis, we reconstituted human H4-mono- to tetra-acetylated nucleosome core particles (NCPs), and solved the crystal structures of the H4-K5/K8/K12/K16-tetra-acetylated NCP and unmodified NCP at 2.4 Å and 2.2 Å resolutions, respectively. The structure of the H4-tetra-acetylated NCP resembled that of the unmodified NCP, and the DNA wrapped the histone octamer as precisely as in the unmodified NCP. However, the B-factors were significantly increased for the peripheral DNAs near the N-terminal tail of the intra- or inter-nucleosomal H4. In contrast, the B-factors were negligibly affected by the H4 tetra-acetylation in histone core residues, including those composing the acidic patch, and at H4-R23, which interacts with the acidic patch of the neighboring NCP. The present study revealed that the H4 tetra-acetylation impairs NCP self-association by changing the interactions of the H4 tail with DNA, and is the first demonstration of crystallization quality NCPs reconstituted with genuine PTMs.
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Affiliation(s)
- Masatoshi Wakamori
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Yoshifumi Fujii
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Noriyuki Suka
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506, Japan
| | - Mikako Shirouzu
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Kensaku Sakamoto
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takashi Umehara
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan,
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan,
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20
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Allahverdi A, Chen Q, Korolev N, Nordenskiöld L. Chromatin compaction under mixed salt conditions: opposite effects of sodium and potassium ions on nucleosome array folding. Sci Rep 2015; 5:8512. [PMID: 25688036 PMCID: PMC4330525 DOI: 10.1038/srep08512] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/07/2015] [Indexed: 01/26/2023] Open
Abstract
It is well known that chromatin structure is highly sensitive to the ionic environment. However, the combined effects of a physiologically relevant mixed ionic environment of K+, Mg2+ and Na+, which are the main cations of the cell cytoplasm, has not been systematically investigated. We studied folding and self-association (aggregation) of recombinant 12-mer nucleosome arrays with 177 bp DNA repeat length in solutions of mixtures of K+ and Mg2+ or Na+ and Mg2+. In the presence of Mg2+, the addition of sodium ions promotes folding of array into 30-nm fibres, whereas in mixtures of K+ and Mg2+, potassium ions abrogate folding. We found that self-association of nucleosome arrays in mixed salt solutions is synergistically promoted by Mg2+ and monovalent ions, with sodium being slightly more efficient than potassium in amplifying the self-association. The results highlight the importance of a mixed ionic environment for the compaction of chromatin under physiological conditions and demonstrate the complicated nature of the various factors that determine and regulate chromatin compaction in vivo.
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Affiliation(s)
- Abdollah Allahverdi
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Qinming Chen
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
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21
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Manduca P, Naim A, Signoriello S. Specific association of teratogen and toxicant metals in hair of newborns with congenital birth defects or developmentally premature birth in a cohort of couples with documented parental exposure to military attacks: observational study at Al Shifa Hospital, Gaza, Palestine. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2014; 11:5208-23. [PMID: 24830451 PMCID: PMC4053911 DOI: 10.3390/ijerph110505208] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/25/2014] [Accepted: 05/04/2014] [Indexed: 01/13/2023]
Abstract
This study was undertaken in Gaza, Palestine, in a cohort of babies born in 2011. Hair samples of newborns were analyzed for metal load by DRC-ICP-MS. We report specific level of contamination by teratogen/toxicants metals of newborn babies, environmentally unexposed, according to their phenotypes at birth: normal full term babies, birth defects or developmentally premature. The occurrence of birth defects was previously shown to be correlated in this cohort to documented exposure of parents to weapons containing metal contaminants, during attacks in 2009. We detect, in significantly higher amounts than in normal babies, different specific teratogen or toxicant elements, known weapons' components, characteristic for each of birth defect or premature babies. This is the first attempt to our knowledge to directly link a phenotype at birth with the in utero presence of specific teratogen and/or toxicant metals in a cohort with known episodes of acute exposure of parents to environmental contamination by these same metals, in this case delivered by weaponry The babies were conceived 20-25 months after the major known parental exposure; the specific link of newborn phenotypes to war-remnant metal contaminants, suggests that mothers' contamination persists in time, and that the exposure may have a long term effect.
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Affiliation(s)
- Paola Manduca
- Dept. Scienze della Terra, Ambientali e della Vita, University of Genoa, Genova 16132, Italy.
| | - Awny Naim
- Palestinina Energy and Natural Resources Authority, Gaza City, Palestine.
| | - Simona Signoriello
- Department of Medical Health and Preventive Medicine, Second University of Naples, Napoli 80100, Italy.
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22
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Musheev MU, Kanoatov M, Krylov SN. Non-uniform velocity of homogeneous DNA in a uniform electric field: consequence of electric-field-induced slow dissociation of highly stable DNA-counterion complexes. J Am Chem Soc 2013; 135:8041-6. [PMID: 23646889 DOI: 10.1021/ja402257x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Identical molecules move with identical velocities when placed in a uniform electric field within a uniform electrolyte. Here we report that homogeneous DNA does not obey this fundamental rule. While most DNA moves with similar velocities, a fraction of DNA moves with velocities that vary within a multiple-fold range. The size of this irregular fraction increases several orders of magnitude when exogenous counterions are added to DNA. The irregular fraction decreases several orders of magnitude when DNA counterions are removed by dialysis against deionized water in the presence of a strong electric field (0.6 kV/cm). Dialysis without the field is ineffective in decreasing the size of irregular fraction. These results suggest that (i) DNA can form very stable complexes with counterions, (ii) these complexes can be dissociated by an electric field, and (iii) the observed non-uniform velocity of DNA is caused by electric-field-induced slow dissociation of these stable complexes. Our findings help to better understand a fundamental property of DNA: its interaction with counterions. In addition, these findings suggest a practical way of making electromigration of DNA more uniform: removal of strongly bound DNA counterions by electro-dialysis against deionized water.
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Affiliation(s)
- Michael U Musheev
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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23
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Abstract
Although it is widely accepted that chronic exposure to arsenite, nickel, chromium and cadmium increases cancer incidence in individuals, the molecular mechanisms underlying their ability to transform cells remain largely unknown. Carcinogenic metals are typically weak mutagens, suggesting that genetic-based mechanisms may not be primarily responsible for metal-induced carcinogenesis. Growing evidence shows that environmental metal exposure involves changes in epigenetic marks, which may lead to a possible link between heritable changes in gene expression and disease susceptibility and development. Here, we review recent advances in the understanding of metal exposure affecting epigenetic marks and discuss establishment of heritable gene expression in metal-induced carcinogenesis.
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Affiliation(s)
- Ricardo Martinez-Zamudio
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
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24
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Wu B, Davey GE, Nazarov AA, Dyson PJ, Davey CA. Specific DNA structural attributes modulate platinum anticancer drug site selection and cross-link generation. Nucleic Acids Res 2011; 39:8200-12. [PMID: 21724603 PMCID: PMC3185412 DOI: 10.1093/nar/gkr491] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Heavy metal compounds have toxic and medicinal potential through capacity to form strong specific bonds with macromolecules, and the interaction of platinum drugs at the major groove nitrogen atom of guanine bases primarily underlies their therapeutic activity. By crystallographic analysis of transition metal-and in particular platinum compound-DNA site selectivity in the nucleosome core, we establish that steric accessibility, which is controlled by specific structural parameters of the double helix, modulates initial guanine-metal bond formation. Moreover, DNA conformational features can be linked to both similarities and distinctions in platinum drug adduct formation between the naked and nucleosomal DNA states. Notably, structures that facilitate initial platinum-guanine bond formation can oppose cross-link generation, rationalizing the occurrence of long-lived therapeutically ineffective monofunctional adducts. These findings illuminate DNA structure-dependent reactivity and provide a novel framework for understanding metal-double helix interactions, which should facilitate the development of improved chromatin-targeting medicinal agents.
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Affiliation(s)
- Bin Wu
- Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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25
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Wu B, Ong MS, Groessl M, Adhireksan Z, Hartinger CG, Dyson PJ, Davey CA. A Ruthenium Antimetastasis Agent Forms Specific Histone Protein Adducts in the Nucleosome Core. Chemistry 2011; 17:3562-6. [DOI: 10.1002/chem.201100298] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Indexed: 01/30/2023]
Affiliation(s)
- Bin Wu
- Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Fax: (+65) 6791‐3856
- Current address: Department of Biological Chemistry and Molecular Pharmacology, Immune Disease Institute, Harvard Medical School, Center for Life Science Building, 3 Blackfan Circle, Boston 02115 (USA)
| | - Michelle S. Ong
- Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Fax: (+65) 6791‐3856
| | - Michael Groessl
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne (Switzerland)
| | - Zenita Adhireksan
- Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Fax: (+65) 6791‐3856
| | - Christian G. Hartinger
- Institute of Inorganic Chemistry, University of Vienna, Waehringer Street 42, 1090 Vienna (Austria)
| | - Paul J. Dyson
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne (Switzerland)
| | - Curt A. Davey
- Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Fax: (+65) 6791‐3856
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26
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Nucleosome structural studies. Curr Opin Struct Biol 2010; 21:128-36. [PMID: 21176878 DOI: 10.1016/j.sbi.2010.11.006] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 11/17/2010] [Accepted: 11/25/2010] [Indexed: 11/22/2022]
Abstract
Chromatin plays a fundamental role in eukaryotic genomic regulation, and the increasing awareness of the importance of epigenetic processes in human health and disease emphasizes the need for understanding the structure and function of the nucleosome. Recent advances in chromatin structural studies, including the first structures of nucleosomes containing the Widom 601 sequence and the structure of a chromatin protein-nucleosome assembly, have provided new insight into stretching of nucleosomal DNA, nucleosome positioning, binding of metal ions, drugs and therapeutic candidates to nucleosomes, and nucleosome recognition by nuclear proteins. These discoveries ensure promising future prospects for unravelling structural attributes of chromatin.
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27
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Allahverdi A, Yang R, Korolev N, Fan Y, Davey CA, Liu CF, Nordenskiöld L. The effects of histone H4 tail acetylations on cation-induced chromatin folding and self-association. Nucleic Acids Res 2010; 39:1680-91. [PMID: 21047799 PMCID: PMC3061077 DOI: 10.1093/nar/gkq900] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Understanding the molecular mechanisms behind regulation of chromatin folding through covalent modifications of the histone N-terminal tails is hampered by a lack of accessible chromatin containing precisely modified histones. We study the internal folding and intermolecular self-association of a chromatin system consisting of saturated 12-mer nucleosome arrays containing various combinations of completely acetylated lysines at positions 5, 8, 12 and 16 of histone H4, induced by the cations Na+, K+, Mg2+, Ca2+, cobalt-hexammine3+, spermidine3+ and spermine4+. Histones were prepared using a novel semi-synthetic approach with native chemical ligation. Acetylation of H4-K16, but not its glutamine mutation, drastically reduces cation-induced folding of the array. Neither acetylations nor mutations of all the sites K5, K8 and K12 can induce a similar degree of array unfolding. The ubiquitous K+, (as well as Rb+ and Cs+) showed an unfolding effect on unmodified arrays almost similar to that of H4-K16 acetylation. We propose that K+ (and Rb+/Cs+) binding to a site on the H2B histone (R96-L99) disrupts H4K16 ε-amino group binding to this specific site, thereby deranging H4 tail-mediated nucleosome–nucleosome stacking and that a similar mechanism operates in the case of H4-K16 acetylation. Inter-array self-association follows electrostatic behavior and is largely insensitive to the position or nature of the H4 tail charge modification.
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Affiliation(s)
- Abdollah Allahverdi
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
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